The models in exp/mono to exp/tri2b utilize the "decode.sh" script. The models in "exp/tri3b" use "decode_fmllr.sh". The fMLLR decoding is a bit involved (requires several steps). The tri2b models are much easier to use - you generally need a single program (after you have the features extracted).
In fact, for tri2b, you can use the "online-wav-gmm-decode-faster" (from src/onlinebin) to decode directly from the WAV.
There are also methods to decode the SAT models in online mode (the online2bin binaries), but you will have to look around for some scripts on how to prepare the proper models for that.
Finally, you can simply reconstruct the "decode.sh" and similar files by hand to see how they work. There are a lot of "if" statements in these scripts since they are designed to work with many different configurations, but if you use a specific model, it's usually a couple of steps that need to be performed for a succesful decode: a couple a programs have to be run, one-by-one. Looking at the decode logs for librispeech will also tell you exactly which program were run and in what order.
Danijel